Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
 
[[WormBase-Caltech_Weekly_Calls_2021|2021 Meetings]]
  
−
= 2022 Meetings =
+
[[WormBase-Caltech_Weekly_Calls_2022|2022 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_January_2022|January]]
+
[[WormBase-Caltech_Weekly_Calls_2023|2023 Meetings]]
  
−
[[WormBase-Caltech_Weekly_Calls_February_2022|February]]
 
  
−
[[WormBase-Caltech_Weekly_Calls_March_2022|March]]
+
==March 14, 2024==
  
−
[[WormBase-Caltech_Weekly_Calls_April_2022|April]]
+
=== TAGC debrief ===
  
−
[[WormBase-Caltech_Weekly_Calls_May_2022|May]]
+
==February 22, 2024==
  
 +
===NER with LLMs===
  
−
= October 6th, 2022 =
+
* Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  
−
== Mangolassi ==
+
* Is this similar to the FlyBase system? Recording of presentation  https://drive.google.com/drive/folders/1S4kZidL7gvBH6SjF4IQujyReVVRf2cOK
−
* Mangolassi is down (network only?); Michael will be in the office in an hour
 
−
** Start a cronjob to check for network connections? Already set up (Raymond)
 
−
** Michael can log into his machine; Tazendra is OK (so, not network issue?)
 
  
−
== GO meeting next week ==
+
* Textpresso server is kaput. Services need to be transferred onto Alliance servers.
−
* 7am - 11am PDT
 
−
* Zoom channel? Available on GO meeting agenda page:
 
−
** https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M
 
  
−
== Alliance Literature working group ==
+
* There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.
−
* Subgroups; Ranjana interested in joining the search subgroup
 
−
* Can sign up on the lit group page
 
−
** https://docs.google.com/document/d/1hB6cft0J_DaapQ9uHUGXwbqrnsZs7wORoepQicLdhTk/edit?pli=1#bookmark=id.butj0rfl4zh1
 
  
−
== Persons ==
+
* Alliance curation status form development needs use cases. ref https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls#February_15.2C_2024
−
* Are there more use cases to collect?
 
−
* Some existing use cases:
 
−
** ACKnowledge attribution
 
−
** Community phenotype curators
 
−
** When do people need person IDs? When accessing/using some forms
 
−
* Content of earlier email
 
−
** When someone asks for a CGC Lab code, they must have a WBPerson ID.  To fill out some tazendra forms, I think they need a WBPerson ID.  To connect Persons to Laboratories for their WB lab page.  To track who is a PI for which Lab.  To connect to other Persons for Intellectual Lineage.  Connect authors to Persons so Papers have a list of authors in publication order, each author linked to the Person (ZFIN has two lists, sorted for authors, separate for persons).  Our users tell us they use the WB Person page for their cv.
 
−
** Use of Person Contact information: I think our use case for person information is mostly to have current emails for community outreach (ACKnowledge, community phenotype forms).  It's been used in the past to send letters to PIs, so we could prioritize maintaining more information just for PIs.  Some analysis is sometimes done by region / country, but this is rare. If anyone can think of other use cases for person data, please let us know. While we mostly only use the email addresses, Cecilia uses address / webpage / ORCID to connect authors to Persons, so having that data is important to make more connections.
 
−
* Knowing address and affiliation can help disambiguate similarly named persons/authors
 
−
* Questions about ethics of tracking information and person lineage?
 
−
** Not really a new issue; people present CVs on grants and other contexts
 
−
** Can be problematic to display people's email address and physical address, from a security perspective
 
−
** Email addresses: if someone has a strain/reagent not in a repository, can be helpful to connect to access materials
 
−
** We and others provide email addresses in publications
 
−
** We don't currently ask for permission to display the information (email, address, etc.)
 
−
** Should we have a survey to ask users' opinions about displaying this information? Is it worthwhile? Concerning?
 
−
** Should we provide a waiver that people agree their information will be in the public domain?
 
−
** Person form disclaimer: "Note: Phone and fax information won't show in your Person report for privacy reasons, but we are collecting the information in case we need to contact you.
 
−
We keep old email, old institution, and old registered_lab data for history, please don't remove it when updating your information."
 
  
−
= Aug 25th, 2022=
 
−
* Phosphoproteomic dataset
 
−
* WB grant - the new and radically different format for a “Biomedical Knowledgebase (U24 - Clinical Trials Not Allowed)” application
 
−
*
 
−
*
 
  
  
 +
==February 15, 2024==
  
 +
=== Literature Migration to the Alliance ABC ===
 +
==== Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)? ====
 +
===== Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic =====
 +
*Facet for topic
 +
*Facet for automatic assertion
 +
**neural network method
 +
*Facet for confidence level
 +
**High
 +
*Facet for manual assertion
 +
**author assertion
 +
***ACKnowledge method
 +
**professional biocurator assertion
 +
***curation tools method - NULL
  
 +
===== Manually validate paper - topic flags without curating =====
 +
*Facet for topic
 +
*Facet for manual assertion
 +
**professional biocurator assertion
 +
***ABC - no data
  
−
= Aug 18th, 2022=  
+
===== View all topic and entity flags for a given paper and validate, if needed =====
−
* Raymond reporting on meeting with Scott Emmons and neural connectivity data
+
* Search ABC with paper identifier
 +
* Migrate to Topic and Entity Editor
 +
* View all associated data
 +
* Manually validate flags, if needed
  
−
= Aug 11th, 2022 =
+
=== PDF Storage ===
 +
* At the Alliance PDFs will be stored in Amazon s3
 +
* We are not planning to formally store back-up copies elsewhere
 +
* Is this okay with everyone?
  
−
Secondary species information content.
+
==February 8, 2024==
−
* Gone through and counted number of objects in different data classes for all species
+
* TAGC
−
* https://docs.google.com/spreadsheets/d/1Q1FE7Miz0IJxultBtEq-VFoAcdz1UpxM3wfER4-qQGg/edit?usp=sharing
+
** Prominent announcement on the Alliance home page?
−
* Pristionchus: Talk to Ralf Sommer and see if wee can take some of the pristionchus.org data into WB -> Ranjana; Decision: after more discussion, decided to hold off on this as the plan is to focus on C. elegans for the grant. Perhaps in the future, we can seek finding and collaboration with the Pritionchus community (such as Sommer lab, etc).
 
  
−
* Brainstorm on how wee can utilize other species data -> may be a separate grant
+
* Fixed login on dockerized system (dev). Can everybody test their forms?
−
* remanei (4 genome versions) and briggsae (3 genome versions) problem -> several versions of the genome. Same problem in parasite. Will need to address in the future. Want to have multiple sequence alignments so researchers can compare different versions.
 
−
* Address c elegans version assemblies in the grant. LoS from authors?
 
−
* Parasite has a new RNAseq analysis pipeline (not single cells yet)
 
  
−
= July 28th, 2022 =
+
==February 1, 2024==
 +
* Paul will ask Natalia to take care of pending reimbursements
 +
* Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.
  
−
Global Core Biodata Resource application
+
==January 25, 2024==
−
https://docs.google.com/document/d/1juJ4mm1evay32lNt3OOsbKL36RY4_3cW/edit?usp=sharing&ouid=106019143058337411488&rtpof=true&sd=true
 
  
 +
=== Curator Info on Curation Forms ===
 +
* Saving curator info using cookies in dockerized forms. Can we deploy to prod?
  
 +
=== ACKnowledge Author Request - WBPaper00066091 ===
 +
* I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  
−
= July 14th, 2022 =
+
* The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.  
−
== Reference and Person Evidence ==
 
−
* We need to know how best to move forward with ?Reference and ?Person evidence in the context of data exchange between WB and the Alliance
 
−
* Does A-team need to connect those WB Persons to be able to populate data in the Alliance curation db ? 
 
−
** If so, can it wait until we have proper persons ? 
 
−
** If not, when we have persons later will the data be reconnected to Person objects ?
 
−
* Where does data come from, which we call Person_evidence ?  Some forms ?  Direct emails ?  Other sources ? 
 
−
* For author curation/verification, what evidence do we want to use?
 
−
* Can we create Paper objects for the actual emails or other forms of communication (figure out details of when and what requirements), but keep Person_evidence for form submissions ?
 
−
* How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs ?
 
−
* If we create personal communication References at Alliance only do we also want them as WBPapers, or will we just keep ?Person evidence at WB?
 
−
* Are we okay with conflating Person data and Paper data in Reference at the Alliance.  That is, duplicating the same data as a Person and as a Reference.
 
  
−
== How to look up balancers (Df / Dp) in WB (PWS/Ryan Baugh) ==
+
* I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  
−
= June 30, 2022 =
+
* Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.
  
−
= June 23, 2022 =
+
=== Update on NN Classification via the Alliance ===
 +
* Use of primary/not primary/not designated flag to filter papers
 +
* Secondary filter on papers with at least C. elegans as species
 +
* Finalize sources (i.e. evidence) for entity and topic tags on papers
 +
* Next NN clasification scheduled for ~March
  
−
Helpdesk tickets
+
* We decided to process all papers (even non-elegans species) and have filters on species after processing.
 +
* NNC html pages will show NNC values together with species.
 +
* Show all C. elegans papers first and other species in a separate bin.
  
−
SOba in Alliance
+
=== Travel Reimbursements ===
 +
* Still waiting on October travel reimbursement (Kimberly)
 +
* Still waiting on September and October travel reimbursements (Wen)
  
−
GCBR application due 8th Aug
+
=== UniProt ===
 +
* Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
 +
* Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
 +
* Stavros escalates the issue on Hinxton Standup.
 +
* Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.
  
−
Prepare for grant; nice pics for metrics eg https://pharos.nih.gov
+
==January 18, 2024==
 +
* OA showing different names highlighted when logging in the OA, now fixed on staging
  
−
Should Alliance gene & allele model have Clone/Sequence name as an attribute?
 
  
 +
==January 11, 2024==
 +
* Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
 +
** Curators should make sure that, when pasting special characters, the duplicate function works
 +
* OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
 +
** If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
 +
* Chris tested on staging and production the phenotype form and the data are still going to tazendra
 +
** Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
 +
** Raymond: simply set up forwarding at our end?
 +
* AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
 +
* Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
 +
* Valerio would like to use an alliancegenome.org email address for the openAI account
 +
* New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
 +
** note: please move shared files that you own to new Alliance Google Drive.  Here is the link to the information that Chris Mungall sent:  For more instructions see the video and SOP here:https://agr-jira.atlassian.net/browse/SCRUM-925?focusedCommentId=40674
 +
* Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
 +
* Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
 +
* Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
 +
* It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
 +
* Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.
  
−
= May 26, 2022 =
+
==January 4, 2024==
−
 
+
* ACKnowlegde pipeline help desk question:
−
WormBase user survey
+
** Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
−
 
+
* Citace upload, current deadline: Tuesday January 9th
−
 
+
** All processes (dumps, etc.) will happen on the cloud machine
−
 
+
** Curators need to deposit their files in the appropriate locations for Wen
−
 
+
* Micropublication pipeline
−
= May 12, 2022 =
+
** Ticketing system confusion
−
 
+
** Karen and Kimberly paper ID pipeline; may need sorting out of logistics
−
==Subcellular localization field==
 
−
* WB has 2 separate free text fields to capture anatomical and subcellular localization statements but obviously the boundaries are fuzzy, see the example below where the statement belongs to both- there are many examples.
 
−
“miR-228 is expressed in the germline and preferentially localizes to the nuclear periphery.”
 
−
 
 
−
* Other MODs do not make such distinction.
 
−
* Daniela is asking the group advice to see if there is any objection in merging the 2 fields and slot the paragraph descriptions in the  ExpressionExperimentStatement in LinkML.
 
−
 
 
−
* Decision: Keep just one field that will take care of both anatomical expression and subcellular localization
 
−
 
 
−
<pre>
 
−
ExpressionExperimentStatement:
 
−
 
 
−
    is_a: EntityStatement
 
−
 
 
−
    description: >-
 
−
 
 
−
      Free-text describing some aspect(s) of a gene's expression, particularly
 
−
 
 
−
      nuanced information that is not readily captured in annotations.
 
−
 
 
−
      This statement's scope is limited to the associated ExpressionExperiment.
 
−
 
 
−
    notes: >-
 
−
 
 
−
      Inherits: statement_subject, statement_type, statement_text, references.
 
−
 
 
−
    slot_usage:
 
−
 
 
−
      statement_subject:
 
−
 
 
−
        range: ExpressionExperiment
 
−
</pre>
 

Revision as of 18:18, 14 March 2024

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings

2018 Meetings

2019 Meetings

2020 Meetings

2021 Meetings

2022 Meetings

2023 Meetings


March 14, 2024

TAGC debrief

February 22, 2024

NER with LLMs

  • Wrote scripts and configured an LLM for Named Entity Recognition. Trained an LLM on gene names and diseases. Works well so far (F1 ~ 98%, Accuracy ~ 99.9%)
  • Textpresso server is kaput. Services need to be transferred onto Alliance servers.
  • There are features on Textpresso, such as link to PDF, that are desirable to curators but should be blocked from public access.


February 15, 2024

Literature Migration to the Alliance ABC

Use Cases for Searches and Validation in the ABC (or, what are your common actions in the curation status form)?

Find papers with a high confidence NN classification for a given topic that have also been flagged positive by an author in a community curation pipeline and that haven’t been curated yet for that topic
  • Facet for topic
  • Facet for automatic assertion
    • neural network method
  • Facet for confidence level
    • High
  • Facet for manual assertion
    • author assertion
      • ACKnowledge method
    • professional biocurator assertion
      • curation tools method - NULL
Manually validate paper - topic flags without curating
  • Facet for topic
  • Facet for manual assertion
    • professional biocurator assertion
      • ABC - no data
View all topic and entity flags for a given paper and validate, if needed
  • Search ABC with paper identifier
  • Migrate to Topic and Entity Editor
  • View all associated data
  • Manually validate flags, if needed

PDF Storage

  • At the Alliance PDFs will be stored in Amazon s3
  • We are not planning to formally store back-up copies elsewhere
  • Is this okay with everyone?

February 8, 2024

  • TAGC
    • Prominent announcement on the Alliance home page?
  • Fixed login on dockerized system (dev). Can everybody test their forms?

February 1, 2024

  • Paul will ask Natalia to take care of pending reimbursements
  • Dockerized system slow pages (OA and FPKMMine). Will monitor these pages in the future. Will look for timeouts in the nginx logs.

January 25, 2024

Curator Info on Curation Forms

  • Saving curator info using cookies in dockerized forms. Can we deploy to prod?

ACKnowledge Author Request - WBPaper00066091

  • I am more than willing to assist; however, the task exceeds the capabilities of the normal flagging process.
  • The paper conducts an analysis of natural variations within 48 wild isolates. To enhance the reliability of the variant set, I utilized the latest variant calling methods along with a custom filtering approach. The resulting dataset comprises 1,957,683 unique variants identified using Clair3. Additionally, Sniffles2 was used to identify indels of >30 bp, which numbered in the thousands to tens of thousands for most wild isolates. It is worth noting that variants identified with Sniffles2 have less reliable nucleotide positions in the genome.
  • I am reaching out to inquire whether WormBase would be interested in incorporating this dataset. An argument in favor is the higher quality of my data. However, I am mindful of the potential substantial effort involved for WormBase, and it is unclear whether this aligns with your priorities.
  • Should WormBase decide to use my variant data set, I am more than willing to offer my assistance.

Update on NN Classification via the Alliance

  • Use of primary/not primary/not designated flag to filter papers
  • Secondary filter on papers with at least C. elegans as species
  • Finalize sources (i.e. evidence) for entity and topic tags on papers
  • Next NN clasification scheduled for ~March
  • We decided to process all papers (even non-elegans species) and have filters on species after processing.
  • NNC html pages will show NNC values together with species.
  • Show all C. elegans papers first and other species in a separate bin.

Travel Reimbursements

  • Still waiting on October travel reimbursement (Kimberly)
  • Still waiting on September and October travel reimbursements (Wen)

UniProt

  • Jae found some genes without uniProt IDs, but the genes are there on uniProt but without WBGene IDs.
  • Wen reached to Stavros and Chris to investigate WormBase and AGR angles.
  • Stavros escalates the issue on Hinxton Standup.
  • Mark checks Build scripts and WS291 results. After that, he contacted UniProt and he's working with them to figure this out.

January 18, 2024

  • OA showing different names highlighted when logging in the OA, now fixed on staging


January 11, 2024

  • Duplicate function in OA was not working when using special characters. Valerio debugged and is now fixed.
    • Curators should make sure that, when pasting special characters, the duplicate function works
  • OA showing different names highlighted when logging in the OA, Valerio will debug and check what IP address he sees
    • If you want to bookmark an OA url for your datatype and user, log on once, and bookmark that page (separately for prod and dev)
  • Chris tested on staging and production the phenotype form and the data are still going to tazendra
    • Chris will check with Paulo. Once it is resolved we need to take everything that is on tazendra and put it on the cloud with different PGIDs
    • Raymond: simply set up forwarding at our end?
  • AI working group: Valerio is setting up a new account for open AI -paid membership for ChatGPT4. We can also use Microsoft Edge copilot (temporary?)
  • Chris getting ready to deploy a 7.0.0. public release - February 7th. Carol wanted to push out monthly releases. This will include WS291. For subsequent releases the next several releases will be WS 291 until WS292 is available.
  • Valerio would like to use an alliancegenome.org email address for the openAI account
  • New alliance drive: https://drive.google.com/drive/folders/0AFkMHZOEQxolUk9PVA
  • Alliance logo and 50 word description for TAGC> Wen will talk to the outreach WG
  • Name server. Manuel working on this, Daniela and Karen will reach out to him and let him know that down the road micropublication would like to use the name server API to generate IDs in bulk
  • Karen asking about some erroneous IDs used in the name server. Stavros says that this is not a big deal because the "reason" is not populating the name server
  • It would be good to be able to have a form to capture additional fields for strains and alleles (see meeting minutes August 31st 2023. https://wiki.wormbase.org/index.php/WormBase-Caltech_Weekly_Calls_2023#August_31st.2C_2023). This may happen after Manuel is done with the authentication.
  • Michael: primary flag with Alliance. Kimberly talked about this with the blue team. They will start bringing that over all papers and fix the remaining 271 items later.

January 4, 2024

  • ACKnowlegde pipeline help desk question:
    • Help Desk: Question about Author Curation to Knowledgebase (Zeng Wanxin) [Thu 12/14/2023 5:48 AM]
  • Citace upload, current deadline: Tuesday January 9th
    • All processes (dumps, etc.) will happen on the cloud machine
    • Curators need to deposit their files in the appropriate locations for Wen
  • Micropublication pipeline
    • Ticketing system confusion
    • Karen and Kimberly paper ID pipeline; may need sorting out of logistics
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